RNA-seq analysis forVishal group at Longwood.

Contact Lorena Pantano (lpantano@hsph.harvard.edu) for additional details.

The most recent update of this html document occurred: Thu May 26 17:49:34 2016

The sections below provide code to reproduce the included results and plots.

Overview

2016-05-26 17:43:12 INFO::Using gene counts calculated from the Sailfish transcript counts.

Quality control metrics

Mapped reads

Genomic mapping rate

Number of genes detected

Gene detection saturation

Exonic mapping rate

rRNA|mitRNA mapping rate

Estimated fragment length of paired-end reads

Boxplot of log10 counts per gene

Boxplot of log10 TMM-normalized counts per gene

Trimmed mean of M-values (TMM) normalization is described here

Robinson, M. D., & Oshlack, A. (2010). A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biology, 11(3). doi:10.1186/gb-2010-11-3-r25

Density of log10 TMM-normalized counts

Correlation (Spearman) heatmap of TMM-normalized counts

MDS plot

Differential expression

Effect of variance stabilization

Dispersion estimates

Comparison: uuo_model


out of 29229 with nonzero total read count
adjusted p-value < 0.1
LFC > 0 (up) : 7234, 25%
LFC < 0 (down) : 6763, 23%
outliers [1] : 63, 0.22%
low counts [2] : 6680, 23%
(mean count < 1)
[1] see ‘cooksCutoff’ argument of ?results
[2] see ‘independentFiltering’ argument of ?results

NULL

Differential expression file at: uuo_model.tsv

Normalized counts matrix file at: uuo_model_log2_counts.tsv

MA plot plot

Volcano plot

QC for DE genes p-values/variance

Most significand, FDR< 0.01 and log2FC > 4 : 855

Plots most significand

Plot top 9 genes

Top DE genes

baseMean log2FoldChange lfcSE stat pvalue padj symbol description day14vsnormal day3vsnormal day7vsnormal absMaxLog2FC
ENSMUSG00000029070 2091.3612 3.465458 0.1452649 551.9509 0 0 Mxra8 matrix-remodelling associated 8 3.465458 1.6290467 2.597665 3.465458
ENSMUSG00000014599 1695.8187 3.508871 0.1486088 547.4308 0 0 Csf1 colony stimulating factor 1 (macrophage) 3.508871 2.7557083 3.630187 3.630187
ENSMUSG00000056025 986.3788 4.484630 0.1887504 529.0076 0 0 Clca3a1 chloride channel accessory 3A1 4.484630 3.0088526 3.940380 4.484630
ENSMUSG00000002020 1384.6000 6.929634 0.2986806 524.6337 0 0 Ltbp2 latent transforming growth factor beta binding protein 2 6.929634 3.5683386 5.345282 6.929634
ENSMUSG00000027188 1124.5795 3.048958 0.1369939 523.5912 0 0 Pamr1 peptidase domain containing associated with muscle regeneration 1 3.048958 1.3219187 2.100980 3.048958
ENSMUSG00000052160 1246.4223 4.438108 0.1824232 496.6850 0 0 Pld4 phospholipase D family, member 4 4.438108 3.3770651 3.712660 4.438108
ENSMUSG00000024610 38169.8961 3.867696 0.1547740 487.0193 0 0 Cd74 CD74 antigen (invariant polypeptide of major histocompatibility complex, class II antigen-associated) 3.867696 2.7307655 3.526930 3.867696
ENSMUSG00000039899 386.9892 4.501820 0.2229482 485.2813 0 0 Fgl2 fibrinogen-like protein 2 4.501820 2.7829065 3.574216 4.501820
ENSMUSG00000027962 8898.3531 6.012705 0.2314572 461.8957 0 0 Vcam1 vascular cell adhesion molecule 1 6.012705 5.4154007 6.291891 6.291891
ENSMUSG00000073490 589.3769 4.437952 0.2063104 454.0854 0 0 AI607873 expressed sequence AI607873 4.437952 3.0902410 3.547935 4.437952
ENSMUSG00000024164 72619.4358 6.908808 0.2662069 448.7313 0 0 C3 complement component 3 6.908808 7.8826994 7.652323 7.882699
ENSMUSG00000041696 794.9974 2.320393 0.1349107 445.6837 0 0 Rasl12 RAS-like, family 12 2.320393 2.7823744 2.665631 2.782374
ENSMUSG00000036905 3421.1210 4.638154 0.2026743 425.4953 0 0 C1qb complement component 1, q subcomponent, beta polypeptide 4.638154 2.6301112 3.727509 4.638154
ENSMUSG00000032000 1470.5987 3.195029 0.1509276 423.9665 0 0 Birc3 baculoviral IAP repeat-containing 3 3.195029 2.6438771 3.182327 3.195029
ENSMUSG00000049037 333.8236 5.106393 0.2819995 422.1968 0 0 Clec4a1 C-type lectin domain family 4, member a1 5.106393 3.1946789 4.323095 5.106393
ENSMUSG00000030772 1628.1774 1.921708 0.1196046 417.1476 0 0 Dkk3 dickkopf WNT signaling pathway inhibitor 3 1.921708 0.0228634 1.233827 1.921708
ENSMUSG00000031875 1843.9338 3.742242 0.1710356 413.4031 0 0 Cmtm3 CKLF-like MARVEL transmembrane domain containing 3 3.742242 2.6701055 3.467449 3.742242
ENSMUSG00000030217 512.6841 3.806288 0.1930331 409.9233 0 0 Art4 ADP-ribosyltransferase 4 3.806288 2.1800739 3.115946 3.806288
ENSMUSG00000055653 6216.8719 3.508102 0.1848132 403.9996 0 0 Gpc3 glypican 3 3.508102 4.0084280 4.316856 4.316856
ENSMUSG00000062980 715.8856 3.408425 0.1812793 399.8000 0 0 Cped1 cadherin-like and PC-esterase domain containing 1 3.408425 1.2519091 2.336112 3.408425

GO ontology of DE genes (log2FC > 4 and FDR < 0.01 ):

ID Description GeneRatio BgRatio pvalue p.adjust qvalue
GO:0030593 GO:0030593 neutrophil chemotaxis 28/684 81/23276 0.0000000 0.0000000 0.0000000
GO:0070098 GO:0070098 chemokine-mediated signaling pathway 20/684 55/23276 0.0000000 0.0000000 0.0000000
GO:0002685 GO:0002685 regulation of leukocyte migration 30/684 155/23276 0.0000000 0.0000000 0.0000000
GO:0006953 GO:0006953 acute-phase response 17/684 41/23276 0.0000000 0.0000000 0.0000000
GO:0002526 GO:0002526 acute inflammatory response 25/684 111/23276 0.0000000 0.0000000 0.0000000
GO:0071347 GO:0071347 cellular response to interleukin-1 19/684 61/23276 0.0000000 0.0000000 0.0000000
GO:0070374 GO:0070374 positive regulation of ERK1 and ERK2 cascade 28/684 166/23276 0.0000000 0.0000000 0.0000000
GO:0002274 GO:0002274 myeloid leukocyte activation 27/684 162/23276 0.0000000 0.0000000 0.0000000
GO:0050707 GO:0050707 regulation of cytokine secretion 26/684 153/23276 0.0000000 0.0000000 0.0000000
GO:0030574 GO:0030574 collagen catabolic process 12/684 24/23276 0.0000000 0.0000000 0.0000000
GO:0032963 GO:0032963 collagen metabolic process 19/684 78/23276 0.0000000 0.0000000 0.0000000
GO:0022409 GO:0022409 positive regulation of cell-cell adhesion 29/684 201/23276 0.0000000 0.0000000 0.0000000
GO:0034341 GO:0034341 response to interferon-gamma 19/684 83/23276 0.0000000 0.0000000 0.0000000
GO:0048520 GO:0048520 positive regulation of behavior 24/684 150/23276 0.0000000 0.0000000 0.0000000
GO:0042129 GO:0042129 regulation of T cell proliferation 23/684 149/23276 0.0000000 0.0000000 0.0000000
GO:0002703 GO:0002703 regulation of leukocyte mediated immunity 23/684 175/23276 0.0000000 0.0000001 0.0000001
GO:0071216 GO:0071216 cellular response to biotic stimulus 26/684 222/23276 0.0000000 0.0000001 0.0000001
GO:1903708 GO:1903708 positive regulation of hemopoiesis 23/684 177/23276 0.0000000 0.0000001 0.0000001
GO:0002449 GO:0002449 lymphocyte mediated immunity 27/684 242/23276 0.0000000 0.0000001 0.0000001
GO:0006909 GO:0006909 phagocytosis 22/684 167/23276 0.0000000 0.0000002 0.0000001
GO:0002573 GO:0002573 myeloid leukocyte differentiation 23/684 185/23276 0.0000000 0.0000002 0.0000002
GO:0030198 GO:0030198 extracellular matrix organization 24/684 210/23276 0.0000000 0.0000005 0.0000004
GO:0007162 GO:0007162 negative regulation of cell adhesion 25/684 230/23276 0.0000000 0.0000007 0.0000005
GO:0030217 GO:0030217 T cell differentiation 25/684 230/23276 0.0000000 0.0000007 0.0000005
GO:0019835 GO:0019835 cytolysis 10/684 33/23276 0.0000000 0.0000007 0.0000005
GO:0042742 GO:0042742 defense response to bacterium 26/684 262/23276 0.0000001 0.0000021 0.0000015
GO:0048771 GO:0048771 tissue remodeling 20/684 163/23276 0.0000001 0.0000022 0.0000016
GO:0045089 GO:0045089 positive regulation of innate immune response 20/684 168/23276 0.0000001 0.0000035 0.0000025
GO:1903035 GO:1903035 negative regulation of response to wounding 19/684 164/23276 0.0000004 0.0000099 0.0000072
GO:0046879 GO:0046879 hormone secretion 28/684 324/23276 0.0000004 0.0000104 0.0000075
GO:0007596 GO:0007596 blood coagulation 19/684 173/23276 0.0000009 0.0000204 0.0000147
GO:0006631 GO:0006631 fatty acid metabolic process 29/684 359/23276 0.0000010 0.0000226 0.0000163
GO:0031639 GO:0031639 plasminogen activation 7/684 21/23276 0.0000015 0.0000303 0.0000219
GO:0031589 GO:0031589 cell-substrate adhesion 24/684 284/23276 0.0000040 0.0000751 0.0000542
GO:0044070 GO:0044070 regulation of anion transport 16/684 141/23276 0.0000041 0.0000771 0.0000556
GO:0016525 GO:0016525 negative regulation of angiogenesis 12/684 81/23276 0.0000042 0.0000772 0.0000557
GO:0042063 GO:0042063 gliogenesis 22/684 259/23276 0.0000092 0.0001512 0.0001090
GO:0002478 GO:0002478 antigen processing and presentation of exogenous peptide antigen 7/684 27/23276 0.0000098 0.0001592 0.0001148
GO:0048871 GO:0048871 multicellular organismal homeostasis 25/684 320/23276 0.0000101 0.0001620 0.0001169
GO:0043491 GO:0043491 protein kinase B signaling 16/684 154/23276 0.0000129 0.0001997 0.0001441
GO:0019233 GO:0019233 sensory perception of pain 14/684 127/23276 0.0000228 0.0003284 0.0002369
GO:0010466 GO:0010466 negative regulation of peptidase activity 19/684 220/23276 0.0000294 0.0004106 0.0002962
GO:0050673 GO:0050673 epithelial cell proliferation 26/684 363/23276 0.0000305 0.0004243 0.0003061
GO:0034113 GO:0034113 heterotypic cell-cell adhesion 8/684 43/23276 0.0000312 0.0004304 0.0003105
GO:0034765 GO:0034765 regulation of ion transmembrane transport 27/684 395/23276 0.0000485 0.0006341 0.0004574
GO:0002507 GO:0002507 tolerance induction 6/684 24/23276 0.0000539 0.0006905 0.0004981
GO:0001503 GO:0001503 ossification 26/684 378/23276 0.0000601 0.0007643 0.0005513
GO:0070206 GO:0070206 protein trimerization 8/684 48/23276 0.0000713 0.0008890 0.0006413
GO:0016053 GO:0016053 organic acid biosynthetic process 20/684 256/23276 0.0000758 0.0009217 0.0006649
GO:0051797 GO:0051797 regulation of hair follicle development 5/684 17/23276 0.0000996 0.0011708 0.0008446
GO:0060541 GO:0060541 respiratory system development 19/684 241/23276 0.0001008 0.0011781 0.0008498
GO:0010876 GO:0010876 lipid localization 22/684 305/23276 0.0001101 0.0012712 0.0009170
GO:0001763 GO:0001763 morphogenesis of a branching structure 18/684 229/23276 0.0001580 0.0017610 0.0012703
GO:0072593 GO:0072593 reactive oxygen species metabolic process 18/684 230/23276 0.0001669 0.0018488 0.0013336
GO:1901616 GO:1901616 organic hydroxy compound catabolic process 8/684 55/23276 0.0001920 0.0020736 0.0014958
GO:0035458 GO:0035458 cellular response to interferon-beta 6/684 30/23276 0.0002047 0.0021798 0.0015724
GO:0006568 GO:0006568 tryptophan metabolic process 4/684 11/23276 0.0002069 0.0021798 0.0015724
GO:0042493 GO:0042493 response to drug 17/684 215/23276 0.0002221 0.0023338 0.0016835
GO:2000108 GO:2000108 positive regulation of leukocyte apoptotic process 6/684 31/23276 0.0002476 0.0025332 0.0018273
GO:0043547 GO:0043547 positive regulation of GTPase activity 19/684 260/23276 0.0002687 0.0027416 0.0019777
GO:0015711 GO:0015711 organic anion transport 23/684 354/23276 0.0003566 0.0035084 0.0025308
GO:0016051 GO:0016051 carbohydrate biosynthetic process 14/684 164/23276 0.0003599 0.0035142 0.0025350
GO:0008202 GO:0008202 steroid metabolic process 19/684 268/23276 0.0003927 0.0037865 0.0027314
GO:1990267 GO:1990267 response to transition metal nanoparticle 9/684 78/23276 0.0004637 0.0043419 0.0031320
GO:0006898 GO:0006898 receptor-mediated endocytosis 15/684 189/23276 0.0004907 0.0045720 0.0032980
GO:0035588 GO:0035588 G-protein coupled purinergic receptor signaling pathway 4/684 15/23276 0.0007791 0.0065993 0.0047604
GO:0042692 GO:0042692 muscle cell differentiation 23/684 376/23276 0.0008177 0.0068893 0.0049697
GO:0061458 GO:0061458 reproductive system development 24/684 412/23276 0.0012452 0.0097083 0.0070031
GO:0006968 GO:0006968 cellular defense response 4/684 17/23276 0.0012963 0.0099859 0.0072034
GO:0033622 GO:0033622 integrin activation 4/684 17/23276 0.0012963 0.0099859 0.0072034

Clustering in common patterns

We used diana function inside cluster R package to separate genes using the expression correlation with time. Clusters with more than 15 genes are shown. A GO and KEGG enrichment is done for each group.

A summary of diana function is copied here:

The diana-algorithm constructs a hierarchy of clusterings, starting with one large cluster containing all n observations. Clusters are divided until each cluster contains only a single observation.
At each stage, the cluster with the largest diameter is selected. (The diameter of a cluster is the largest dissimilarity between any two of its observations.)
To divide the selected cluster, the algorithm first looks for its most disparate observation (i.e., which has the largest average dissimilarity to the other observations of the selected cluster). This observation initiates the "splinter group". In subsequent steps, the algorithm reassigns observations that are closer to the "splinter group" than to the "old party". The result is a division of the selected cluster into two new clusters.


Working with  855  genes

Working with 855 genes.

group: 1

ID Description GeneRatio BgRatio pvalue p.adjust qvalue
mmu05150 mmu05150 NA 17/159 51/6698 0.0000000 0.0000000 0.0000000
mmu04060 mmu04060 NA 28/159 246/6698 0.0000000 0.0000000 0.0000000
mmu05323 mmu05323 NA 14/159 85/6698 0.0000000 0.0000003 0.0000002
mmu05146 mmu05146 NA 16/159 116/6698 0.0000000 0.0000003 0.0000002
mmu04062 mmu04062 NA 20/159 189/6698 0.0000000 0.0000003 0.0000002
mmu05140 mmu05140 NA 12/159 65/6698 0.0000000 0.0000005 0.0000004
mmu04145 mmu04145 NA 19/159 179/6698 0.0000000 0.0000006 0.0000004
mmu04514 mmu04514 NA 15/159 154/6698 0.0000031 0.0000416 0.0000288
mmu04640 mmu04640 NA 11/159 83/6698 0.0000035 0.0000416 0.0000288
mmu04380 mmu04380 NA 13/159 118/6698 0.0000038 0.0000416 0.0000288
mmu04650 mmu04650 NA 13/159 125/6698 0.0000072 0.0000695 0.0000481
mmu05332 mmu05332 NA 9/159 58/6698 0.0000075 0.0000695 0.0000481
mmu05144 mmu05144 NA 8/159 47/6698 0.0000121 0.0001033 0.0000715
mmu04940 mmu04940 NA 9/159 63/6698 0.0000151 0.0001138 0.0000788
mmu05310 mmu05310 NA 6/159 24/6698 0.0000154 0.0001138 0.0000788
mmu05020 mmu05020 NA 6/159 35/6698 0.0001494 0.0010366 0.0007176
mmu04512 mmu04512 NA 9/159 86/6698 0.0001839 0.0012006 0.0008311
mmu05330 mmu05330 NA 7/159 56/6698 0.0003248 0.0020030 0.0013866
mmu04672 mmu04672 NA 6/159 45/6698 0.0006164 0.0034696 0.0024019
mmu04612 mmu04612 NA 8/159 81/6698 0.0006252 0.0034696 0.0024019
mmu05322 mmu05322 NA 11/159 152/6698 0.0009243 0.0048857 0.0033822
mmu04610 mmu04610 NA 7/159 76/6698 0.0020605 0.0103960 0.0071969
mmu04621 mmu04621 NA 6/159 58/6698 0.0023775 0.0114740 0.0079431
mmu04620 mmu04620 NA 8/159 101/6698 0.0026338 0.0116941 0.0080955
mmu05142 mmu05142 NA 8/159 101/6698 0.0026338 0.0116941 0.0080955
mmu05143 mmu05143 NA 4/159 32/6698 0.0065507 0.0279665 0.0193604
mmu05320 mmu05320 NA 6/159 72/6698 0.0069955 0.0287591 0.0199091
mmu04510 mmu04510 NA 11/159 200/6698 0.0078135 0.0309751 0.0214432
mmu05014 mmu05014 NA 5/159 56/6698 0.0102021 0.0370666 0.0256601
mmu04974 mmu04974 NA 6/159 78/6698 0.0102422 0.0370666 0.0256601
mmu04630 mmu04630 NA 9/159 153/6698 0.0103519 0.0370666 0.0256601
mmu04664 mmu04664 NA 6/159 80/6698 0.0115296 0.0399934 0.0276863
mmu04080 mmu04080 NA 13/159 277/6698 0.0141966 0.0477521 0.0330574
ID Description GeneRatio BgRatio pvalue p.adjust qvalue
GO:0030593 GO:0030593 neutrophil chemotaxis 24/400 81/23276 0.0000000 0.0000000 0.0000000
GO:0097529 GO:0097529 myeloid leukocyte migration 29/400 152/23276 0.0000000 0.0000000 0.0000000
GO:0070098 GO:0070098 chemokine-mediated signaling pathway 15/400 55/23276 0.0000000 0.0000000 0.0000000
GO:0032103 GO:0032103 positive regulation of response to external stimulus 29/400 289/23276 0.0000000 0.0000000 0.0000000
GO:1903037 GO:1903037 regulation of leukocyte cell-cell adhesion 28/400 268/23276 0.0000000 0.0000000 0.0000000
GO:0002443 GO:0002443 leukocyte mediated immunity 30/400 313/23276 0.0000000 0.0000000 0.0000000
GO:0050727 GO:0050727 regulation of inflammatory response 28/400 271/23276 0.0000000 0.0000000 0.0000000
GO:0002274 GO:0002274 myeloid leukocyte activation 22/400 162/23276 0.0000000 0.0000000 0.0000000
GO:0002687 GO:0002687 positive regulation of leukocyte migration 19/400 117/23276 0.0000000 0.0000000 0.0000000
GO:0019221 GO:0019221 cytokine-mediated signaling pathway 29/400 314/23276 0.0000000 0.0000000 0.0000000
GO:0032963 GO:0032963 collagen metabolic process 16/400 78/23276 0.0000000 0.0000000 0.0000000
GO:1902105 GO:1902105 regulation of leukocyte differentiation 25/400 249/23276 0.0000000 0.0000000 0.0000000
GO:0002250 GO:0002250 adaptive immune response 29/400 372/23276 0.0000000 0.0000000 0.0000000
GO:0050707 GO:0050707 regulation of cytokine secretion 19/400 153/23276 0.0000000 0.0000000 0.0000000
GO:0002237 GO:0002237 response to molecule of bacterial origin 26/400 316/23276 0.0000000 0.0000000 0.0000000
GO:0048520 GO:0048520 positive regulation of behavior 17/400 150/23276 0.0000000 0.0000000 0.0000000
GO:1903708 GO:1903708 positive regulation of hemopoiesis 18/400 177/23276 0.0000000 0.0000001 0.0000000
GO:0002253 GO:0002253 activation of immune response 23/400 295/23276 0.0000000 0.0000001 0.0000001
GO:0006897 GO:0006897 endocytosis 30/400 495/23276 0.0000000 0.0000001 0.0000001
GO:0030198 GO:0030198 extracellular matrix organization 19/400 210/23276 0.0000000 0.0000002 0.0000001
GO:0050708 GO:0050708 regulation of protein secretion 25/400 391/23276 0.0000000 0.0000007 0.0000005
GO:0042742 GO:0042742 defense response to bacterium 19/400 262/23276 0.0000002 0.0000041 0.0000028
GO:0048002 GO:0048002 antigen processing and presentation of peptide antigen 10/400 67/23276 0.0000002 0.0000052 0.0000036
GO:0042060 GO:0042060 wound healing 21/400 326/23276 0.0000003 0.0000064 0.0000044
GO:0032890 GO:0032890 regulation of organic acid transport 9/400 60/23276 0.0000008 0.0000173 0.0000120
GO:0043491 GO:0043491 protein kinase B signaling 13/400 154/23276 0.0000028 0.0000518 0.0000359
GO:0043547 GO:0043547 positive regulation of GTPase activity 17/400 260/23276 0.0000030 0.0000546 0.0000379
GO:0007229 GO:0007229 integrin-mediated signaling pathway 9/400 76/23276 0.0000062 0.0001029 0.0000713
GO:0051797 GO:0051797 regulation of hair follicle development 5/400 17/23276 0.0000076 0.0001228 0.0000850
GO:0019233 GO:0019233 sensory perception of pain 11/400 127/23276 0.0000126 0.0001950 0.0001351
GO:2000108 GO:2000108 positive regulation of leukocyte apoptotic process 6/400 31/23276 0.0000127 0.0001950 0.0001351
GO:0043588 GO:0043588 skin development 16/400 265/23276 0.0000157 0.0002337 0.0001619
GO:0060541 GO:0060541 respiratory system development 15/400 241/23276 0.0000202 0.0002948 0.0002042
GO:0060346 GO:0060346 bone trabecula formation 4/400 11/23276 0.0000258 0.0003602 0.0002495
GO:0001503 GO:0001503 ossification 19/400 378/23276 0.0000337 0.0004557 0.0003157
GO:0034765 GO:0034765 regulation of ion transmembrane transport 19/400 395/23276 0.0000608 0.0007541 0.0005223
GO:0033622 GO:0033622 integrin activation 4/400 17/23276 0.0001713 0.0018024 0.0012484
GO:0042303 GO:0042303 molting cycle 9/400 119/23276 0.0002190 0.0022531 0.0015606
GO:0042692 GO:0042692 muscle cell differentiation 17/400 376/23276 0.0003042 0.0030345 0.0021018
GO:0061458 GO:0061458 reproductive system development 18/400 412/23276 0.0003086 0.0030694 0.0021260
GO:0010817 GO:0010817 regulation of hormone levels 19/400 466/23276 0.0004979 0.0045892 0.0031787
GO:0044708 GO:0044708 single-organism behavior 19/400 472/23276 0.0005811 0.0052669 0.0036481
GO:0045104 GO:0045104 intermediate filament cytoskeleton organization 5/400 41/23276 0.0006585 0.0057303 0.0039690
GO:0016049 GO:0016049 cell growth 19/400 483/23276 0.0007651 0.0064191 0.0044461

group: 2

ID Description GeneRatio BgRatio pvalue p.adjust qvalue
mmu04610 mmu04610 NA 4/24 76/6698 0.0001369 0.0053405 0.0046126
mmu04620 mmu04620 NA 4/24 101/6698 0.0004104 0.0080035 0.0069126
mmu05150 mmu05150 NA 3/24 51/6698 0.0007521 0.0097768 0.0084442
ID Description GeneRatio BgRatio pvalue p.adjust qvalue
GO:0006953 GO:0006953 acute-phase response 7/85 41/23276 0.00e+00 0.0000002 0.0000002
GO:0002526 GO:0002526 acute inflammatory response 8/85 111/23276 0.00e+00 0.0000059 0.0000046
GO:0060326 GO:0060326 cell chemotaxis 8/85 224/23276 1.70e-06 0.0008845 0.0006921
GO:0055072 GO:0055072 iron ion homeostasis 5/85 69/23276 5.40e-06 0.0021638 0.0016930
GO:0006935 GO:0006935 chemotaxis 10/85 491/23276 1.21e-05 0.0033540 0.0026242
GO:0070371 GO:0070371 ERK1 and ERK2 cascade 7/85 255/23276 4.16e-05 0.0074745 0.0058482

group: 3

ID Description GeneRatio BgRatio pvalue p.adjust qvalue
mmu04060 mmu04060 NA 7/22 246/6698 0.0000088 0.0003520 0.0002779
mmu04145 mmu04145 NA 4/22 179/6698 0.0024744 0.0402005 0.0317372
mmu04062 mmu04062 NA 4/22 189/6698 0.0030150 0.0402005 0.0317372
ID Description GeneRatio BgRatio pvalue p.adjust qvalue
GO:0030595 GO:0030595 leukocyte chemotaxis 6/53 166/23276 0.0000021 0.0015717 0.0010672
GO:0050727 GO:0050727 regulation of inflammatory response 7/53 271/23276 0.0000026 0.0015717 0.0010672
GO:0002526 GO:0002526 acute inflammatory response 5/53 111/23276 0.0000054 0.0015717 0.0010672
GO:0002292 GO:0002292 T cell differentiation involved in immune response 4/53 53/23276 0.0000065 0.0015717 0.0010672
GO:0007159 GO:0007159 leukocyte cell-cell adhesion 8/53 476/23276 0.0000114 0.0020326 0.0013801
GO:1902107 GO:1902107 positive regulation of leukocyte differentiation 5/53 143/23276 0.0000185 0.0024975 0.0016957
GO:0042517 GO:0042517 positive regulation of tyrosine phosphorylation of Stat3 protein 3/53 28/23276 0.0000351 0.0032838 0.0022296
GO:0006935 GO:0006935 chemotaxis 7/53 491/23276 0.0001186 0.0052874 0.0035900
GO:0010466 GO:0010466 negative regulation of peptidase activity 5/53 220/23276 0.0001430 0.0059557 0.0040438
GO:1903532 GO:1903532 positive regulation of secretion by cell 6/53 389/23276 0.0002480 0.0083567 0.0056740
GO:0006957 GO:0006957 complement activation, alternative pathway 2/53 11/23276 0.0002761 0.0084016 0.0057045

group: 4

ID Description GeneRatio BgRatio pvalue p.adjust qvalue
mmu00380 mmu00380 NA 6/66 45/6698 0.0000044 0.0003328 0.0002443
mmu00650 mmu00650 NA 5/66 31/6698 0.0000111 0.0003655 0.0002683
mmu00140 mmu00140 NA 6/66 55/6698 0.0000144 0.0003655 0.0002683
mmu00982 mmu00982 NA 6/66 87/6698 0.0001965 0.0037331 0.0027404
mmu00983 mmu00983 NA 5/66 59/6698 0.0002645 0.0040210 0.0029517
mmu00120 mmu00120 NA 3/66 15/6698 0.0003821 0.0048399 0.0035528
mmu00500 mmu00500 NA 4/66 45/6698 0.0009459 0.0091772 0.0067367
mmu00830 mmu00830 NA 5/66 78/6698 0.0009660 0.0091772 0.0067367
mmu00053 mmu00053 NA 3/66 25/6698 0.0018002 0.0146592 0.0107609
mmu00590 mmu00590 NA 5/66 91/6698 0.0019288 0.0146592 0.0107609
mmu00250 mmu00250 NA 3/66 33/6698 0.0040372 0.0278478 0.0204423
mmu00260 mmu00260 NA 3/66 34/6698 0.0043970 0.0278478 0.0204423
mmu04146 mmu04146 NA 4/66 80/6698 0.0077640 0.0440135 0.0323091
mmu03320 mmu03320 NA 4/66 81/6698 0.0081078 0.0440135 0.0323091
ID Description GeneRatio BgRatio pvalue p.adjust qvalue
GO:0006631 GO:0006631 fatty acid metabolic process 15/134 359/23276 0.0000000 0.0000030 0.0000026
GO:0044283 GO:0044283 small molecule biosynthetic process 16/134 448/23276 0.0000000 0.0000041 0.0000035
GO:0044282 GO:0044282 small molecule catabolic process 12/134 245/23276 0.0000000 0.0000075 0.0000065
GO:0009072 GO:0009072 aromatic amino acid family metabolic process 5/134 25/23276 0.0000003 0.0000566 0.0000487
GO:0043252 GO:0043252 sodium-independent organic anion transport 5/134 28/23276 0.0000005 0.0000628 0.0000540
GO:0008202 GO:0008202 steroid metabolic process 10/134 268/23276 0.0000036 0.0001830 0.0001574
GO:0015711 GO:0015711 organic anion transport 11/134 354/23276 0.0000067 0.0003161 0.0002718
GO:0005996 GO:0005996 monosaccharide metabolic process 9/134 243/23276 0.0000119 0.0005032 0.0004327
GO:0044262 GO:0044262 cellular carbohydrate metabolic process 9/134 263/23276 0.0000223 0.0009093 0.0007820
GO:0006639 GO:0006639 acylglycerol metabolic process 6/134 101/23276 0.0000263 0.0010362 0.0008910
GO:1990267 GO:1990267 response to transition metal nanoparticle 5/134 78/23276 0.0000884 0.0028204 0.0024254
GO:0006833 GO:0006833 water transport 3/134 16/23276 0.0000989 0.0030711 0.0026410
GO:1901361 GO:1901361 organic cyclic compound catabolic process 9/134 331/23276 0.0001312 0.0039711 0.0034149
GO:0034377 GO:0034377 plasma lipoprotein particle assembly 3/134 21/23276 0.0002300 0.0058998 0.0050735

R Session Info

(useful if replicating these results)

R version 3.3.0 (2016-05-03)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux stretch/sid

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    parallel  methods   stats     graphics  grDevices utils    
[8] datasets  base     

other attached packages:
 [1] hexbin_1.27.1              vsn_3.40.0                
 [3] DEGreport_1.5.0            quantreg_5.24             
 [5] SparseM_1.7                dplyr_0.4.3               
 [7] cluster_2.0.4              org.Mm.eg.db_3.3.0        
 [9] AnnotationDbi_1.34.3       clusterProfiler_3.0.2     
[11] DOSE_2.10.2                gridExtra_2.2.1           
[13] logging_0.7-103            tximport_1.0.2            
[15] DESeq2_1.12.2              SummarizedExperiment_1.2.2
[17] Biobase_2.32.0             GenomicRanges_1.24.0      
[19] GenomeInfoDb_1.8.1         IRanges_2.6.0             
[21] S4Vectors_0.10.1           BiocGenerics_0.18.0       
[23] pheatmap_1.0.8             CHBUtils_0.1              
[25] edgeR_3.14.0               limma_3.28.5              
[27] gplots_3.0.1               reshape_0.8.5             
[29] ggplot2_2.1.0              myRfunctions_0.1          
[31] knitr_1.13                 rmarkdown_0.9.6           
[33] BiocInstaller_1.22.2      

loaded via a namespace (and not attached):
 [1] bitops_1.0-6          matrixStats_0.50.2    RColorBrewer_1.1-2   
 [4] tools_3.3.0           affyio_1.42.0         R6_2.1.2             
 [7] rpart_4.1-10          KernSmooth_2.23-15    Hmisc_3.17-4         
[10] DBI_0.4-1             colorspace_1.2-6      nnet_7.3-12          
[13] preprocessCore_1.34.0 Nozzle.R1_1.1-1       chron_2.3-47         
[16] graph_1.50.0          formatR_1.4           topGO_2.24.0         
[19] caTools_1.17.1        scales_0.4.0          affy_1.50.0          
[22] genefilter_1.54.2     stringr_1.0.0         digest_0.6.9         
[25] foreign_0.8-66        XVector_0.12.0        htmltools_0.3.5      
[28] RSQLite_1.0.0         BiocParallel_1.6.2    gtools_3.5.0         
[31] acepack_1.3-3.3       GOSemSim_1.30.2       magrittr_1.5         
[34] GO.db_3.3.0           Formula_1.2-1         Matrix_1.2-6         
[37] Rcpp_0.12.5           munsell_0.4.3         stringi_1.0-1        
[40] yaml_2.1.13           zlibbioc_1.18.0       plyr_1.8.3           
[43] qvalue_2.4.2          grid_3.3.0            gdata_2.17.0         
[46] DO.db_2.9             lattice_0.20-33       splines_3.3.0        
[49] annotate_1.50.0       locfit_1.5-9.1        igraph_1.0.1         
[52] geneplotter_1.50.0    reshape2_1.4.1        XML_3.98-1.4         
[55] evaluate_0.9          latticeExtra_0.6-28   data.table_1.9.6     
[58] MatrixModels_0.4-1    gtable_0.2.0          tidyr_0.4.1          
[61] assertthat_0.1        xtable_1.8-2          coda_0.18-1          
[64] survival_2.39-4       GSEABase_1.34.0